esetLda {esetVis} | R Documentation

## plot a biplot of a linear discriminant analysis of an eSet object

### Description

`esetLda` reduces the dimension of the data contained in the eSet via a linear discriminant analysis on the specified grouping variable with the `lda` function and plot the subsequent biplot, possibly with sample annotation and gene annotation contained in the eSet.

### Usage

    esetLda(eset, ldaVar, psids = 1:nrow(eset), dim = c(1, 2),
      colorVar = character(), color = if (length(colorVar) == 0) "black"
      else character(), shapeVar = character(), shape = if
      (length(shapeVar) == 0) 15 else numeric(), sizeVar = character(),
      size = if (length(sizeVar) == 0) {     ifelse(typePlot == "interactive"
      && length(packageInteractivity) == 1 && packageInteractivity == "rbokeh",
      5, 2.5) } else {     numeric() }, sizeRange = numeric(),
      alphaVar = character(), alpha = if (length(alphaVar) == 0) 1 else
      numeric(), alphaRange = numeric(), title = "",
      symmetryAxes = c("combine", "separate", "none"),
      packageTextLabel = c("ggrepel", "ggplot2"), cloudGenes = TRUE,
      cloudGenesColor = "black", cloudGenesNBins = sqrt(length(psids)),
      cloudGenesIncludeLegend = FALSE, cloudGenesTitleLegend = "nGenes",
      topGenes = 10, topGenesCex = 2.5, topGenesVar = character(),
      topGenesJust = c(0.5, 0.5), topGenesColor = "black",
      topSamples = 10, topSamplesCex = 2.5, topSamplesVar = character(),
      topSamplesJust = c(0.5, 0.5), topSamplesColor = "black",
      geneSets = list(), geneSetsVar = character(),
      geneSetsMaxNChar = numeric(), topGeneSets = 10,
      topGeneSetsCex = 2.5, topGeneSetsJust = c(0.5, 0.5),
      topGeneSetsColor = "black", includeLegend = TRUE,
      includeLineOrigin = TRUE, typePlot = c("static", "interactive"),
      packageInteractivity = c("rbokeh", "ggvis"),
      figInteractiveSize = c(600, 400), ggvisAdjustLegend = TRUE,
      interactiveTooltip = TRUE, interactiveTooltipExtraVars = character(),
      returnAnalysis = FALSE, returnEsetPlot = FALSE)

### Arguments

`eset` | expressionSet (or SummarizedExperiment) object with data
`ldaVar` | name of variable (in varLabels of the `eset`) used for grouping for lda
`psids` | featureNames of genes to include in the plot, all by default
`dim` | dimensions of the analysis to represent, first two dimensions by default
`colorVar` | name of variable (in varLabels of the `eset`) used for coloring, empty by default
`color` | character or factor with specified color(s) for the points, replicated if needed. This is used only if `colorVar` is empty. By default: 'black' if `colorVar` is not specified and default `ggplot` palette otherwise
`shapeVar` | name of variable (in varLabels of the `eset`) used for the shape, empty by default
`shape` | character or factor with specified shape(s) (pch) for the points, replicated if needed. This is used only if `shapeVar` is empty. By default: '15' (filled square) if `shapeVar` is not specified and default `ggplot` shape(s) otherwise
`sizeVar` | name of variable (in varLabels of the `eset`) used for the size, empty by default
`size` | character or factor with specified size(s) (cex) for the points, replicated if needed. This is used only if `sizeVar` is empty. By default: '2.5' if `sizeVar` is not specified and default `ggplot` size(s) otherwise
`sizeRange` | size (cex) range used in the plot, possible only if the `sizeVar` is 'numeric' or 'integer'
`alphaVar` | name of variable (in varLabels of the `eset`) used for the transparency, empty by default. This parameter is currently only available for static plot and ggvis (only numeric in this case).
`alpha` | character or factor with specified transparency(s) for the points, replicated if needed. This is used only if `shapeVar` is empty. By default: '1' if `alphaVar` is not specified and default `ggplot` alpha otherwise This parameter is currently only available for static and ggvis.
`alphaRange` | transparency (alpha) range used in the plot, possible only if the `alphaVar` is 'numeric' or 'integer' This parameter is currently only available for static and ggvis plot.
`title` | plot title, ” by default
`symmetryAxes` | set symmetry for axes, either: 'combine' (by default): both axes are symmetric and with the same limits 'separate': each axis is symmetric and has its own limits 'none': axes by default (plot limits)
`packageTextLabel` | package used to label the outlying genes/samples/gene sets, either `ggrepel` (by default, only used if package `ggrepel` is available), or `ggplot2`
`cloudGenes` | logical, if TRUE (by default), include the cloud of genes in the plot
`cloudGenesColor` | if `cloudGenes` is TRUE, color for the cloud of genes, black by default
`cloudGenesNBins` | number of bins to used for the clouds of genes, by default the square root of the number of genes
`cloudGenesIncludeLegend` | logical, if TRUE (FALSE by default) include the legend for the cloud of genes (in the top position if multiple legends)
`cloudGenesTitleLegend` | string with title for the legend for the cloud of genes 'nGenes' by default
`topGenes` | numeric indicating which percentile (if <1) or number (if >=1) of genes most distant to the origin of the plot to annotate, by default: 10 genes are selected If no genes should be annotated, set this parameter to 0 Currently only available for static plot.
`topGenesCex` | cex for gene annotation (used when `topGenes` > 0)
`topGenesVar` | variable of the featureData used to label the genes, by default: empty, the featureNames are used for labelling (used when `topGenes` > 0)
`topGenesJust` | text justification for the genes (used when `topGenes` > 0 and if `packageTextLabel` is `ggplot2`), by default: c(0.5, 0.5) so centered
`topGenesColor` | text color for the genes (used when `topGenes` > 0), black by default
`topSamples` | numeric indicating which percentile (if <1) or number (if >=1) of samples most distant to the origin of the plot to annotate, by default: 10 samples are selected If no samples should be annotated, set this parameter to 0. Currently available for static plot.
`topSamplesCex` | cex for sample annotation (used when `topSamples` > 0)
`topSamplesVar` | variable of the phenoData used to label the samples, by default: empty, the sampleNames are used for labelling (used when `topSample`s > 0)
`topSamplesJust` | text justification for the samples (used when `topSamples` > 0 and if `packageTextLabel` is `ggplot2`), by default: c(0.5, 0.5) so centered
`topSamplesColor` | text color for the samples (used when `topSamples` > 0), black by default
`geneSets` | list of gene sets/pathways, each containing identifiers of genes contained in the set. E.g. pathways from Gene Ontology databases output from the `getGeneSetsForPlot` function or any custom list of pathways. The genes identifiers should correspond to the variable `geneSetsVar` contained in the phenoData, if not specified the featureNames are used. If several gene sets have the same name, they will be combine to extract the top gene sets.
`geneSetsVar` | variable of the featureData used to match the genes contained in geneSets, most probably ENTREZID, if not specified the featureNames of the eSet are used Only used when `topGeneSets` > 0 and the parameter geneSets is specified.
`geneSetsMaxNChar` | maximum number of characters for pathway names, by default keep entire names Only used when `topGeneSets` > 0 and the parameter `geneSets` is specified. If `returnAnalysis` is set to TRUE and `geneSetsMaxNChar` specified, the top pathways will be returned in the output object, named with the identifiers used in the plot (so with maximum `geneSetsMaxNChar` number of characters)
`topGeneSets` | numeric indicating which percentile (if <=1) or number (if >1) of gene sets most distant to the origin of the plot to annotate, by default: 10 gene sets are selected If no gene sets should be annotated, set this parameter to 0. Currently available for static plot. Only used when `topGeneSets` > 0 and the parameter geneSets is specified.
`topGeneSetsCex` | cex for gene sets annotation Only used when `topGeneSets` > 0 and the parameter geneSets is specified.
`topGeneSetsJust` | text justification for the gene sets by default: c(0.5, 0.5) so centered Only used when `topGeneSets` > 0, the parameter `geneSets` is specified and if `packageTextLabel` is `ggplot2`.
`topGeneSetsColor` | color for the gene sets (used when `topGeneSets` > 0 and `geneSets` is specified), black by default Only used when `topGeneSets` > 0 and the parameter geneSets is specified.
`includeLegend` | logical if TRUE (by default) include a legend, otherwise not
`includeLineOrigin` | if TRUE (by default) include vertical line at x = 0 and horizontal line at y = 0
`typePlot` | type of the plot returned, either 'static' (static) or interactive' (potentially interactive)
`packageInteractivity` | if `typePlot` is 'interactive', package used for interactive plot, either 'rbokeh' (by default) or 'ggvis'
`figInteractiveSize` | vector containing the size of the interactive plot, as [width, height] by default: c(600, 400). This is passed to the `width` and `height` parameters of: for rbokeh plots: the `bokeh::figure` function for ggvis plots: the `ggvis::set_options` function
`ggvisAdjustLegend` | logical, if TRUE (by default) adjust the legends in `ggvis` to avoid overlapping legends when multiple legends
`interactiveTooltip` | logical, if TRUE, add hoover functionality showing sample annotation (variables used in the plot) in the plot
`interactiveTooltipExtraVars` | name of extra variable(s) (in varLabels of the `eset`) to add in rbokehEsetPlot to label the samples, empty by default
`returnAnalysis` | logical, if TRUE (FALSE by default), return also the output of the analysis, and the outlying samples in the topElements element if any, otherwise only the plot object
`returnEsetPlot` | logical, if TRUE return also the esetPlot object

### Value

if `returnAnalysis` is TRUE, return a list:

- analysis: output of the spectral map analysis, whose parameters can be given as input to the `esetPlotWrapper` function

  - dataPlotSamples: coordinates of the samples

  - dataPlotGenes: coordinates of the genes

  - esetUsed: expressionSet used in the plot

- topElements: list with top outlying elements if any, possibly genes, samples and gene sets

- plot: the plot output

otherwise return only the plot

### Author(s)

Laure Cougnaud

### References

Fisher, R. A. (1936). The Use of Multiple Measurements in Taxonomic Problems. Annals of Eugenics, 7 (2), 179–188

### See Also

the function used internally: `lda`

### Examples

    # load data
    library(ALL)
    data(ALL)

    # specify several variables in ldaVar (this might take a few minutes to run...)

    # sample subsetting: currently cannot deal with missing values
    samplesToRemove <- which(apply(pData(ALL)[, c("sex", "BT")], 1, anyNA))

    # extract random features, because analysis is quite time consuming
    retainedFeatures <- sample(featureNames(ALL), size = floor(nrow(ALL)/5))

    # create the plot
    esetLda(eset = ALL[retainedFeatures, -samplesToRemove],
      ldaVar = "BT", colorVar = "BT", shapeVar = "sex", sizeVar = "age",
      title = "Linear discriminant analysis on the ALL dataset")

[Package esetVis version 1.12.0 Index]